From 9f70b504e29deca2c1524ce4da810f60906945e5 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Thu, 19 Oct 2023 11:23:41 -0500
Subject: [PATCH] feat: Add fasterq-dump module

---
 modules/fasterq_dump/main.nf | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 modules/fasterq_dump/main.nf

diff --git a/modules/fasterq_dump/main.nf b/modules/fasterq_dump/main.nf
new file mode 100644
index 0000000..560d113
--- /dev/null
+++ b/modules/fasterq_dump/main.nf
@@ -0,0 +1,25 @@
+process FASTERQ_DUMP {
+    tag "${prefix} (${sra})"
+    label 'process_single'
+
+    container 'quay.io/biocontainers/sra-tools:3.0.8--h9f5acd7_0'
+
+    input:
+    tuple val(prefix), val(sra)
+
+    output:
+    tuple val(prefix), path("*.fastq.gz")
+
+    publishDir "${params.outdir}/${task.process}", mode: 'copy'
+
+    script:
+    """
+    fasterq-dump \\
+            --verbose \\
+            --concatenate-reads \\
+            --stdout \\
+            ${sra} \\
+        | gzip \\
+        > "${prefix}.fastq.gz"
+    """
+}